Introduction ? Project 1 We appreciate the concerns of the reviewers, and have modified our project accordingly in many aspects. Major changes between previous and current proposals include i) In June, for family reasons, Dr. Zawada accepted a position in the department of neurology at UColorado. ii) Toward tighter integration of the projects, the PD mouse model work has been supplanted by analysis of the BRI-A?42 model used in Project 2. iii) Hypothesis has changed focus to neuronal stress and microglial response interactions as governed by APOE genotype, favoring resilience or dysfunction, and ways in which drugs can intervene in these processes. iv) As previously proposed animal models and experiments are no longer proposed in this iteration, any reviewer concerns dealing with these animal models are not considered in this introduction. ??why the investigators do not simply examine all of the markers in all human brain regions examined...? Taking the advice of the reviewer, we have decided to pursue this course, and have added the proposed brain regions to Aim 1. ?How many human brains will be examined per condition?? A more detailed answer is elaborated in Core B?s introduction, but, in brief, based on biostatistical power analysis on our expected effect sizes, we plan to study 6 brains per condition, with more to be added if necessary. ?Will quantitative IHF be performed at UAMC and IBC or both?...? This will be performed at both institutions. This is now explained in detail in the introduction to Core B, but in brief, in our long-term collaboration, we have maintained laboratories with similar skills and identical procedures. Images will be captured at their respective sites, but experimental quantitation will be performed by Project 1 personnel at UAMS. ?How will the data be analyzed? Labeling intensity, stereological counts, percent immunoreactivity within a field? Which statistical tests will be employed?? Much of this has been addressed in the re-written Project 1, however, labeling intensity will be the principle measure in IF/IHC data, with statistical analyses tailored to the question being asked. In some cases, intensity-per-field analyses will be sufficient, in which case images will be averaged over the whole area and each case will be considered one data point. In other cases, cell-by-cell intensity measures will be necessary, or even subcellular localizations, such as nuclear NEDD8 translocation. Most disease vs. control data will be analyzed by t-test with ?=0.05, and error bars will be reported as SEM. ??using an antibody against P2yR12 might be useful in the Aim 1 studies.? Taking the advice of the reviewer, we will add P2yR12 antibodies to analyses in both Aim 1 and Aim 3. ??The distinction between Project 1 work and Core work needs to be made clearer (e.g. what will Project 1 personnel do on Aim 1?).? The staining and initial evaluation of the tissue integrity, as well as image capture, will be performed by Core B personnel at UAMS or ICL. Analysis of data, experimental design, statistical tests, and interpretation of results will be performed by Project 1 personnel. Manuscript preparation will involve relevant Project and Core members. ?Readouts are unclear?, ?The specifics? were not well defined in the first aim?? Taking the reviewer?s advice, greater care has been taken in the Approach to clearly delineate exactly what will be measured and their interpretations, including numbers, Braak stage, and comorbidities. ??in Aim one, any observations will necessarily remain correlational.? As is always the case in human autopsy material, only correlational data can be gleaned. This concern is addressed by complementary in vitro and in vivo experiments to strengthen the correlative nature of Aim 1. However, we believe it is the goal of in vitro and in vivo studies to mimic human conditions, making it imperative to understand in the detail we can in experimental settings and what we see in human disease. ??that the studies will provide ?the first systematic? relationship to the neuroinflammatory [aspects in AD, etc? ] This is not clear in the experimental plan... this concern was addressed by Dr. Griffin.? We have clarified our experimental plan in each of the aims we now propose, and have added much new data to support the validity of pursuing our hypothesis and have provided more detail regarding methodology and analysis, including which diseases are studied, and the regions to be examined. ?The PL has not set criteria for [prioritization]? for drug selection.? Our goal here is to inform Core D as we reveal disease-related mechanisms in Aim 1. In view of the new data presented here as preliminary work, we are already coordinating with Core D for the design of specific BBB-permeant drugs directed toward inflammatory and proteostasis pathways. These are now proposed to be tested in Aim 2d and Projects 2 and 3.